Seems to me your main block should look more like:

#!/usr/bin/perl -w use strict; my @main = &open_file_main (); my @annot = &open_file_annot (); open OUTPUT, '>', 'output.txt' or die "Cannot open $!"; # loop through the main data file foreach my $md (@main) { chomp $md; my ($main_chrom, $winl, $winr) = split (/\s{2,}/, $md); foreach my $ad (@annot) { my ($an_chrom, undef, undef, $prol, $pror, undef, undef, undef +, $mess) = split (/\s{2,}/, $ad); next unless $main_chrom eq $an_chrom; my (undef, undef, $name) = split (/\;/, $mess); next if $winr < $prol or $winl > $pror; print OUTPUT "$name\t $md\n"; #last; } } exit;

Note that there is no need for a sub to open the output file! If you need to do complicated stuff in the context of opening the output file, return the file handle from the sub - do not use a 'global' variable that is set as a side effect!


Perl is environmentally friendly - it saves trees

In reply to Re: Faulty Control Structures? by GrandFather
in thread Faulty Control Structures? by bioinformatics

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post; it's "PerlMonks-approved HTML":



  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.